Is the scientist begging the question? No. The scientist is stating a fact.”

You’re partially correct. In the empirical sense he isn’t begging the question at all, but he is begging the question in the non-empirical sense.

He assumes that only material causes are involved because that’s all empirical studies are concerned with. Ask an expert in non-empirical studies and he’ll tell you the scientist’s statement begs the question wrt the final cause.

Imagine a jungle tribe. It knows nothing of gravity. They believe in a god who pulls things toward earth. They believe they must sacrifice to this god. They believe by praying to this god they can reduce his effects and they can jump higher. When they occasionally see airplanes fly overhead, it is a miracle from their god.

A scientist visits the tribe and learns of this god. He says, “Gravity is caused by an attractive force between atoms. In every single case, gravity has a non-supernatural explanation, because your gravity god is imaginary.”

Is the scientist begging the question? No. The scientist is stating a fact.